. Author manuscript; available in PMC: 2013 Sep 1.

Published in final edited form as: Alcohol Clin Exp Res. 2012 Jun 15;36(9):1512–1518. doi: 10.1111/j.1530-0277.2012.01758.x

Table 3.

Associations of CNVs and alcohol dependence

Locus^a	CNV type	CNV frequency			Beta ^b	P value ^c	Genes
Locus^a	CNV type		Cases	Controls	Beta ^b	P value ^c	Genes
Chr5: 68,921,426-70,412,247	Copy number/dosage^e	Duplication	43 (4.97%)	16 (1.59%)	0.69	3.37 × 10⁻⁴	SMA4, SERF1, SERF1B, SMN2, SMA3, NAIP, GTF2H2, GTF2H2D, OCLN ^d
		Deletion	22 (2.54%)	36 (3.57%)
		Non-missing	865 (100%)	1008 (100%)

chr6:79,034,386-79,090,197	Duplication	Duplication	83 (8.99%)	38 (3.49%)	1.05	1.04 × 10⁻⁶	Gene desert
		Deletion	448 (48.54%)	542 (49.77%)
		Non-missing	923 (100%)	1089 (100%)

The starting and the ending point are defined by the probes whose P values have a clear deviation from the rest.

^b.c

The P value and beta of this region is annotated by the most significant probe in this CNV.

OCLN is located less than 30 kb downstream of this region.

This CNV was analyzed as ≤1= deletion, 2=normal diploid, ≥3=duplication. For cases: Deletions: 4/22 had a dosage score of 0.667 (18/22 had a score of 1, or heterozygous for deletion); Duplications: 39/43 had a dosage score of 3 (heterozygous) and the remainder had a mean score of 3.3. For controls: Deletions: 11/36 had a dosage score of 0.667, remainder scoring 1; Duplications: 13/22 had a dosage score of 3, 2/22 had a score of 3.3 and 1/22 had a score of 4 (homozygous duplication).